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Fix missing leading zeros in the concept_codes for Treatment NAACCR item codes. #60

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mgurley opened this issue Aug 21, 2019 · 3 comments

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@mgurley
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mgurley commented Aug 21, 2019

There is a consistent problem of missing leading zeros in the concept_code column of NAACCR treatment variables:
1390, 1400, 1410,1506,1516,1526.

For example, the concept_code for OMOP concept_id = 35918602 is '1390@1'. It should be instead '1390@01'. This problem is consistent across the board for the NAACCR treatment variables. See here documentation that the leading zeros are necessary:
http://datadictionary.naaccr.org/default.aspx?c=10#1390
http://datadictionary.naaccr.org/default.aspx?c=10#1400
http://datadictionary.naaccr.org/default.aspx?c=10#1410
http://datadictionary.naaccr.org/default.aspx?c=10#1506
http://datadictionary.naaccr.org/default.aspx?c=10#1516
http://datadictionary.naaccr.org/default.aspx?c=10#1526

Here are the troublemakers that are missing a leading zero in the naaccr_item_code_omop_concept_code

naaccr_item_omop_concept_id naaccr_item_omop_concep_name naaccr_item_omop_concept_code naaccr_item_omop_concept_class_id naaccr_item_code_omop_concept_id naaccr_item_code_omop_concept_name naaccr_item_code_omop_concept_code
35918602 RX Summ--Chemo 1390 35915215 Chemotherapy, NOS. 1390@1
35918602 RX Summ--Chemo 1390 35916302 Chemotherapy, single agent. 1390@2
35918602 RX Summ--Chemo 1390 35918919 Chemotherapy, multiple agents. 1390@3
35918619 RX Summ--Hormone 1400 35918922 Hormone therapy administered as first course therapy. 1400@1
35918454 RX Summ--BRM 1410 35918935 Immunotherapy administered as first course therapy. 1410@1
35918686 Phase I Radiation Treatment Modality 1506 35918951 External beam, NOS 1506@1
35918686 Phase I Radiation Treatment Modality 1506 35918969 External beam, photons 1506@2
35918686 Phase I Radiation Treatment Modality 1506 35918953 External beam, protons 1506@3
35918686 Phase I Radiation Treatment Modality 1506 35918970 External beam, electrons 1506@4
35918686 Phase I Radiation Treatment Modality 1506 35919009 External beam, neutrons 1506@5
35918686 Phase I Radiation Treatment Modality 1506 35916381 Brachytherapy, NOS 1506@7
35918686 Phase I Radiation Treatment Modality 1506 35918989 Brachytherapy, intracavitary, LDR 1506@8
35918686 Phase I Radiation Treatment Modality 1506 35918971 Brachytherapy, intracavitary, HDR 1506@9
35918378 Phase II Radiation Treatment Modality 1516 35918975 External beam, NOS 1516@1
35918378 Phase II Radiation Treatment Modality 1516 35918959 External beam, photons 1516@2
35918378 Phase II Radiation Treatment Modality 1516 35918946 External beam, protons 1516@3
35918378 Phase II Radiation Treatment Modality 1516 35919006 External beam, electrons 1516@4
35918378 Phase II Radiation Treatment Modality 1516 35918964 External beam, neutrons 1516@5
35918378 Phase II Radiation Treatment Modality 1516 35918952 Brachytherapy, NOS 1516@7
35918378 Phase II Radiation Treatment Modality 1516 35918945 Brachytherapy, intracavitary, LDR 1516@8
35918378 Phase II Radiation Treatment Modality 1516 35918990 Brachytherapy, intracavitary, HDR 1516@9
35918255 Phase III Radiation Treatment Modality 1526 35919013 External beam, NOS 1526@1
35918255 Phase III Radiation Treatment Modality 1526 35919000 External beam, photons 1526@2
35918255 Phase III Radiation Treatment Modality 1526 35918974 External beam, protons 1526@3
35918255 Phase III Radiation Treatment Modality 1526 35918948 External beam, electrons 1526@4
35918255 Phase III Radiation Treatment Modality 1526 35919011 External beam, neutrons 1526@5
35918255 Phase III Radiation Treatment Modality 1526 35918995 Brachytherapy, NOS 1526@7
35918255 Phase III Radiation Treatment Modality 1526 35918997 Brachytherapy, intracavitary, LDR 1526@8
35918255 Phase III Radiation Treatment Modality 1526 35919007 Brachytherapy, intracavitary, HDR 1526@9
@mgurley mgurley changed the title Fix missing leading zeros in answers for NAACCR treatment variables. Fix missing leading zeros in the concept_codes for for NAACCR item codes. Aug 21, 2019
@mgurley mgurley changed the title Fix missing leading zeros in the concept_codes for for NAACCR item codes. Fix missing leading zeros in the concept_codes for NAACCR item codes. Aug 21, 2019
@mgurley mgurley changed the title Fix missing leading zeros in the concept_codes for NAACCR item codes. Fix missing leading zeros in the concept_codes for Treatment NAACCR item codes. Aug 28, 2019
@dimshitc
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dimshitc commented Sep 2, 2019

also changing all these '<Proc_schema>@1290@0' to '<Proc_schema>@1290@00'

@mgurley
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mgurley commented Sep 2, 2019

@dimshitc

My list forgot to include the following concept_codes: '1506@06', '1516@06' and '1526@06' . Can you make sure these have the leading zeros as well?

@mgurley
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mgurley commented Sep 19, 2019

This is done.

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